Is the a way to select everything that's inside a circles area? For example, I put 4 objects inside the circle, run the script, and all the objects move with it. Then I can put other objects into it, run the script, and move the circle and all the objects move with it. Any suggestions would be amazing.

no, seriously, a circle is 2D, and your scene world is 3D. what constitutes an object being "in" the circle? does the circle define an infinitely long invisible tube? or a sphere? or is it only those objects who are bisected by the circle?

This could be way off the mark but...in theory it seems like it could work.
Looking for way to have swapable parenting at that level seems like it could get crazy.
What about a group of lattices.
One for each row vertically.
One for each row horizontally.
Not sure if it would be better to have each cube as a separate piece of geo or maybe try combining all your cubes into one and lattice them.
As with most things like this in maya you never know for sure until you try.
I wonder...Hmmm.

EDIT:
NOPE...just tried it...it works at first but then the deformation order goes crazy when trying to rotate things too much.
Good luck!

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